Final run

[RichRick1]

I have fixed few things:

1. Now toml files utils should work as expected.
2. I fixed the functionality of the PariserParr module, specifically compute_U and, related to it, compute_gamma functions. Now, compute_U function takes argument ionization_dictionary as input, as opposed to atom_dictionary that we had before. Also, we don't estimate the ionization, we either read it from file, or use values provided by user; compute_gamma function assumes now that everything is connected with everything instead of looking only at connectivity provided by user.
3. I tweaked tutorial a little bit, so it reflect all of the changes above.